Chromosomes are organized structures of DNA and protein and are present in nearly every cell in our body. Each chromosome contains hundreds of genes that determine many of our exhibited personal traits, such as eye color, hair color and the like. Typically, humans have two sets of twenty-three chromosomes, one set of which is acquired from our mother and the other of which is acquired from our father.
While humans ordinarily have two copies of each autosomal region, this may vary for particular genetic regions due to DNA copy loss or gain. Many times, such loss or gain is normal and does not adversely affect the person. Unfortunately, other times such loss or gain is associated with a genetic syndrome or disorder. For instance, Down syndrome (or Trisomy 21) is a genetic disorder that is caused by the presence of some or all of an extra twenty-first chromosome. Other genetic disorders that are caused by chromosomal DNA copy loss or gain include, among others, Cri du chat, Wolf-Hirschhorn syndrome, Edward's syndrome, Jacobsen syndrome and Turner syndrome.
Currently, over 100 regions of human chromosomes are known to be associated with well-described genetic syndromes that are caused by DNA copy loss or gain. Many of these imbalances are sub-microscopic, which requires the use of complex technologies to detect these imbalances in a patient's genome. One such technology, known as array-based comparative genomic hybridization (“array CGH” or “aCGH”), has proven effective at allowing researchers, doctors and clinicians to rapidly evaluate chromosomal segment losses and gains.
To perform array CGH, a doctor or clinician extracts DNA from a patient sample. This DNA is then tagged with a fluorescent dye. A control sample from another person, meanwhile, is also prepared and tagged with a fluorescent dye of a different color. This control sample is typically taken from a person who does not exhibit any traits of a genetic disorder or syndrome. That is, the control sample should typically comprise a representation of a “normal” genome. At this point, the patient DNA and the control DNA are mixed together on a microscope slide (known as a “microarray slide”) that may have, for instance, thousands of regions of chromosomes represented as dots on the slide. Each of these dots contains unique fragments of DNA from a particular section of each chromosome.
Once the patient and control DNA are applied to the microarray slide, fragments of the patient and control DNA compete to attach (or “hybridize”) to the DNA fragments in each dot of the microarray slide. For each location on the slide, if the patient DNA does not have a gain or a loss, then the patient DNA should compete equally with the control DNA (assuming that the control DNA also does not have a gain or a loss at that location). If, however, the patient DNA has a loss at that location, then the control DNA will hybridize to the DNA fragment to a greater degree than will the patient DNA. Conversely, if the patient DNA has a gain, then the patient DNA will hybridize to the DNA fragment to a greater degree than will the control DNA.
After hybridization occurs, the microarray slide may be placed in a scanner that measures the fluorescent signals of each microarray dot. In instances where the patient and the control compete equally, the distinct fluorescent colors will result in the appearance of a color that reflects equal dosage of the two colors. In instances where a patient has a loss, however, the scan will result in the predominance of the fluorescent color with which the control DNA was tagged. Conversely, where the patient DNA has a gain, the scan will result in the predominance of the fluorescent color with which the patient DNA was tagged. With this information, a doctor or a clinician may determine where the patient has chromosomal segments gains and/or losses. Furthermore, with this knowledge, the doctor or clinician may formulate or verify a diagnosis for the patient. For instance, the doctor or clinician may use this information to verify (to a higher degree of certainty) that a particular patient does indeed have Down syndrome.
Given ongoing research as well as application in clinical settings, different users may make use of different terminology. For example, “patient” and “study subject” are considered synonymous, with the distinction being point of view. Researchers typically refer to an individual under investigation as a “study subject” while doctors and clinicians refer to the individual under investigation as a “patient.” Similarly, a researcher may generate “experimental results” on the study subject while doctors and clinicians generate “test results” on a patient.
While array CGH and other technologies have drastically improved clinician's ability to detect DNA copy gains and losses, a need exists to leverage previously-accumulated knowledge and experience.